final lecuter content for bich e1

How stable is a native protein compared with its unfolded form?

Only marginally more stable under physiological conditions (~0.4 kJ/mol per amino acid).

What interactions stabilize protein tertiary structure?

Hydrophobic interactions, electrostatic interactions, hydrogen bonds, chemical crosslinking, and metal ions.

What is the major driving force behind protein folding?

The hydrophobic effect: nonpolar residues minimize contact with water by becoming buried in the protein interior.

How does hydropathy predict amino acid location in a globular protein?

High hydropathy (nonpolar) residues favor the interior; low/negative hydropathy (polar) residues favor the exterior.

What are salt bridges, and why is their contribution to protein stability limited?

Electrostatic interactions between oppositely charged groups; their stabilizing effect is limited by an unfavorable decrease in entropy.

Why do hydrogen bonds make relatively minor contributions to overall protein stability?

Unfolded proteins can also form hydrogen bonds with water, limiting the net stabilization from protein hydrogen bonds.

Where are disulfide bonds more common: intracellular or secreted proteins?

Secreted proteins, because the extracellular environment is oxidizing; the intracellular environment is generally reducing.

What are the four major causes of protein denaturation?

Heat, extreme pH, detergents, and chaotropic agents.

What happens to protein function during denaturation?

Loss of native structure generally results in loss of function.

What is the denaturation temperature (Tm)?

The temperature at which folded and unfolded states are equally favorable: ΔG = 0 and ΔH = TΔS.

What did Anfinsen's ribonuclease A experiment demonstrate?

A denatured protein can spontaneously refold into its native, active structure when appropriate conditions are restored.

What reagents were used to denature and reduce ribonuclease A in Anfinsen's experiment?

8 M urea disrupts noncovalent interactions; β-mercaptoethanol reduces disulfide bonds.

Why can ribonuclease A become trapped in an inactive, scrambled state?

Incorrect disulfide bonds form, preventing the protein from adopting its native structure.

What does protein disulfide isomerase (PDI) do?

Reduces and reoxidizes disulfide bonds to correct non-native disulfide bonds and facilitate proper protein folding.

What are the functions of reduced versus oxidized PDI?

Reduced PDI rearranges non-native disulfide bonds; oxidized PDI catalyzes initial disulfide bond formation.

What information determines a protein's native structure under physiological conditions?

Its primary amino acid sequence contains the information needed to adopt its native higher-order structure.

What is Levinthal's paradox?

Proteins fold rapidly despite having too many possible conformations to sample every one randomly.

What is the hierarchical model of protein folding?

Local secondary structures form first, followed by higher-order tertiary and quaternary structures.

What is the hydrophobic collapse model of protein folding?

Hydrophobic interactions drive rapid collapse into a compact molten globule with a hydrophobic core.

How do proteins generally fold according to the two folding models?

Through a combination of hierarchical folding and hydrophobic collapse.

What does a protein-folding funnel represent?

Progression toward lower free energy and the stable native conformation; folding is favorable when ΔG < 0.

What do hills and valleys in a folding funnel represent?

Free-energy barriers and intermediate conformations in which proteins may become temporarily trapped.

What is the function of molecular chaperones?

They bind unfolded or partially folded proteins, reduce aggregation, and facilitate proper folding.

What are the two major classes of molecular chaperones discussed in lecture?

The Hsp70 family and chaperonins.

How does the Hsp70/DnaK system use ATP and ADP?

ATP hydrolysis promotes tight binding to an unfolded protein; ADP release and ATP rebinding allow protein release.

What are the functions of DnaJ and GrpE in the Hsp70 system?

DnaJ helps deliver unfolded proteins to DnaK and stimulates ATP hydrolysis; GrpE promotes ADP release.

What is the function of the GroEL/GroES chaperonin system?

It provides an ATP-dependent, protected environment in which proteins can fold without aggregating.

What are the possible outcomes of protein misfolding?

Refolding into the native structure, degradation, or aggregation that may contribute to disease.

What protein is affected in hereditary emphysema, and what is the consequence?

α1-antitrypsin; slow folding allows its target, elastase, to damage lung tissue.

What is the difference between normal and abnormal prion protein?

PrPᶜ: mainly α-helical, soluble, and protease-sensitive. PrPˢᶜ: β-structure-rich, insoluble, and protease-resistant.

How does abnormal prion protein propagate?

PrPˢᶜ converts normal PrPᶜ into the abnormal conformation, leading to protein aggregation.

Which prion diseases are associated with humans, cattle, and sheep?

Humans: Creutzfeldt–Jakob disease. Cattle: mad cow disease. Sheep: scrapie.

What is the origin of β-amyloid peptide, and how is it associated with Alzheimer's disease?

β-Amyloid is derived from amyloid precursor protein (APP); it forms β-sheet-rich aggregates and plaques in neural tissue.

What protein is affected in cystic fibrosis, and what happens to its folding?

CFTR; unstable folding intermediates can be degraded before the protein functions properly.

What is the normal function of CFTR?

An epithelial chloride-ion channel that helps regulate water movement and maintain thin, freely flowing mucus.

Why does defective CFTR cause thick, sticky mucus?

Impaired chloride transport disrupts water movement, producing abnormally thick mucus in organs such as the lungs and pancreas.